I'm sympathetic to some of your concerns, but have you tried playing a game and not upgrading harvesters? Do you like it more? As someone said above, I do think it's true that AI War is kind of a toolkit for making the game you want; if you take every advantage you can squeeze out of it it's not as much fun as letting it throw some surprises at you. On that note, I feel like it might be worth trying starting off with the bonus ships you don't like and not hacking ARS's, too --- do you not think it might be more fun for you to have to cope with some ships you don't want?
Yes, I have tried games where I haven't upgraded harvesters, and no, I don't like it more, though I also don't like it much less. That doesn't mean that it isn't a strategic choice - in choosing between harvesters and fleet ships, I'm making a choice between having the ability to field one strong fleet which I can slowly replace, or a weaker fleet that I can replace more quickly. There are advantages and disadvantages to both, and how much fun one is as compared to the other depends very much on how well you can handle downtime if you just lost a big chunk of your fleet. Having a fleet with three times the firepower from the start is a very big advantage over upgrading your harvesters, and if you take advantage of it you can probably gain as much benefit as you would have from having upgraded your harvesters - for one thing, you now have a whole bunch of Mark I ships that are relatively disposable, and whose loss will not cripple your fleet. Hence, an excellent supply of guerrilla ships, and, at least until the AIP and knowledge gains catch up with your choice of early military power over early economic strength, you have a relatively easier time than you would if you chose harvester upgrades. Certainly, the early game becomes slower due to the lackluster economy, but this is at least partially made up by not needing to build turrets for defense - if you have caps of Mark I and Mark II ships, and you're used to using a fully Mark I fleet at this point in the game, then you could:
1) Leave the Mark IIs at home, and have a very strong defense force
2) Leave the Mark Is at home, and have an offensive fleet that's roughly twice as strong as what you usually have
3) Leave an equivalent to the Mark I cap at home, and send out two offensive groups each about as strong as your normal Mark I fleet
4) Etc.
My preferred early unlocks are one harvester to mark 3, and then one or two fleet ships to mark II, and decide what to do with the leftovers later. I also go for both harvesters to mark 3, and neither harvester to mark 3. All of these choices work (at least for me), and each has their own advantages and disadvantages. I'd say that the biggest disadvantage that not unlocking any harvester upgrades has is that it makes the early game slower. Later in the game, it doesn't matter as much as you're going to have a fairly high metal and crystal income, anyways, so at that point the higher income is relatively less important than in the early game. The biggest disadvantage of the economic choice is that I have fewer disposable forces early on, and it's early in the game that I'm most inclined to make raids with small forces to draw the special forces away, or to hit some valuable target. Thus, since I like to have a strong economy, and I also like to have a military force that can afford to treat some units as disposable, I usually compromise between a full-economic opening and a full-military opening. Certainly, by making such a compromise I have more difficulty replacing losses than I would if I'd gone for a full-economic opening, but I also have more ships available, and I have some ships that I can detach from my main fleet without significantly affecting my main fleet's fighting strength. Compared to a full-military opening, I don't have as many relatively disposable ships, but I am also able to replace losses more quickly, and I'll attain my full fleet strength faster (though my full fleet strength is less than what it would be if I'd gone for a full-military opening). These are very much strategic-level decisions, which have a direct impact on both the tactical level of the game and on my strategy for the near future. Full military? I'd best make use of that, and try to capture some planets quickly to make up for the lacking aspects of my economy. I might also be better able to engage the special forces, or I could sacrifice my Mark I ships as a distraction while my Mark II ships go liberate something special, or I could split groups off to go raiding while the main body stays home while I slowly build turrets and prepare for an assault on a target. Full economy? Now it's the other end of the early game spectrum - I can quickly replace ships, but I don't have the military strength to directly challenge strong targets and I want to have many turrets up quickly so I don't need to keep my Mark I fleet at home.
Choosing military strength is also, at least to a point, advantageous if you want to have a discontiguous empire, because with more and stronger warships, you can be in more places at once and still have roughly the same strength present as you would if you were to concentrate the majority of your force in one spot in a game where you chose economic over military strength.
I also rarely bother hacking ARS's. I don't find it generally worth the bother of dealing with the spawns, and it also can be fun to try out new ship types. It can be fun to make use of a tried and true ship, but it can also be very boring if I have the same ships game after game.
I wonder. How early in the game do you needt o have a signifigant presence in a special forces defended planet to make them completely irrelevant? If you could, in theory, get enough units to take and hold a planet that the special forces deems important, and do so for the rest of the game.. Would that not make the entire special forces ai basically useless on the defense?
No idea. My usual method of dealing with the special forces early on is to try to get them to go hunt a raiding group, and then send my main group after wherever it was I wanted to attack and needed the special forces out of the way in order to do so.